The thesis studies and analyses the most important factors influencing marine pollution by black waters from vessels. Distribution of sanitary waste waters on board and their damaging effect onto people, marine life and economy have been explored. Indicators of marine pollution by faecal waters have been identified. International, regional and national regulations governing black water treatment on board have been analysed as well as non-conformities with the regulations. Equipment for collection and treatment of black waters on board was tested in operation on both the small and large vessels. The recommended IMO and ISO models for risk assessment were tested and analysed. After testing the existing models were found as inadequate for assessment of the risk of pollution by black waters from vessels, consequently, an original model was installed for risk assessment. After installation the original model was implemented for risk assessment on different types of vessels. The original risk assessment model utilizes several important factors, such as risk index for different types of vessels and sensitivity index for different locations. The size of each index depends on the input factors. The risk assessment results for marine pollution by different vessels on different locations confirmed the main scientific hypothesis, i.e. the cruise ships are in the low risk category, while smaller vessels, such as boats and yachts are in the high risk category for pollution of coastal seas by black waters. Validity of the proposed model was tested in the experimental part of the thesis. Sea water samples were collected on different locations in the target typical coastal area (Dubrovnik), with the marine traffic involving different types of vessels, within the period of 14 months and submitted for analysis with regard to faecal marine pollution indicators. Scientific (statistical) analysis of the sample analysis results and the number of vessels of different types at particular locations was applied. The analysis of the results indicates that there is a correlation between the marine pollution indicators (faecal coliform bacteria) with the smaller vessels (boats and yachts) on particular locations. It has also been found that there is no correlation between the cruise ships and bacteria on these ships’ routes. Consequently, the results of the sea sampling and chi-square tests have confirmed without any doubt not only the main scientific hypothesis but also the validity of the model for risk assessment of marine pollution by black waters from vessels. The final chapter of the thesis suggests recommendations for better protection against this type of marine pollution. Adoption of new regulation on protection against marine pollution by faecal waters from vessels, yachts and boats sailing in internal waters and territorial seas has been recommended. Measures to be applied by the county and local authorities have been proposed as well as recommendations for vessel owners on upgrade of their equipment and treatment of black waters on board their vessels.